The Plant Microbiome: From Ecology to Reductionism and beyond

Connor R. Fitzpatrick, Isai Salas-González, Jonathan M. Conway, Omri M. Finkel, Sarah Gilbert, Dor Russ, Paulo José Pereira Lima Teixeira, Jeffery L. Dangl

Research output: Contribution to journalReview articlepeer-review

153 Scopus citations


Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.

Original languageEnglish (US)
Pages (from-to)81-100
Number of pages20
JournalAnnual Review of Microbiology
StatePublished - Sep 8 2020
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Microbiology


  • Plant microbiome
  • microbial adaptation
  • microbiome assembly
  • plant exudates
  • plant immunity


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